VTK  9.1.0
vtkMoleculeReaderBase.h
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1 /*=========================================================================
2 
3  Program: Visualization Toolkit
4  Module: vtkMoleculeReaderBase.h
5 
6  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
7  All rights reserved.
8  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
9 
10  This software is distributed WITHOUT ANY WARRANTY; without even
11  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12  PURPOSE. See the above copyright notice for more information.
13 
14 =========================================================================*/
27 #ifndef vtkMoleculeReaderBase_h
28 #define vtkMoleculeReaderBase_h
29 
30 #include "vtkIOChemistryModule.h" // For export macro
31 #include "vtkPolyDataAlgorithm.h"
32 
33 class vtkCellArray;
34 class vtkFloatArray;
35 class vtkDataArray;
36 class vtkIdTypeArray;
39 class vtkPoints;
40 class vtkStringArray;
41 class vtkMolecule;
42 class vtkPeriodicTable;
43 
44 class VTKIOCHEMISTRY_EXPORT vtkMoleculeReaderBase : public vtkPolyDataAlgorithm
45 {
46 public:
48  void PrintSelf(ostream& os, vtkIndent indent) override;
49 
52 
54 
57  vtkSetMacro(BScale, double);
58  vtkGetMacro(BScale, double);
60 
62 
65  vtkSetMacro(HBScale, double);
66  vtkGetMacro(HBScale, double);
68 
72  vtkGetMacro(NumberOfAtoms, vtkIdType);
73 
77  vtkGetMacro(NumberOfModels, unsigned int);
78 
79 protected:
82 
83  char* FileName;
84  double BScale;
85  double HBScale;
87  unsigned int NumberOfModels;
88 
91 
100  int ReadMolecule(FILE* fp, vtkPolyData* output);
101 
110  unsigned int MakeAtomType(const char* atomType);
111 
121  unsigned int MakeBonds(vtkPoints* points, vtkIdTypeArray* atomTypes, vtkCellArray* newBonds);
122 
137 
138  virtual void ReadSpecificMolecule(FILE* fp) = 0;
139 
140 private:
142  void operator=(const vtkMoleculeReaderBase&) = delete;
143 };
144 
145 #endif
object to represent cell connectivity
Definition: vtkCellArray.h:181
abstract superclass for arrays of numeric data
Definition: vtkDataArray.h:50
dynamic, self-adjusting array of float
Definition: vtkFloatArray.h:36
dynamic, self-adjusting array of vtkIdType
a simple class to control print indentation
Definition: vtkIndent.h:34
Store zero or more vtkInformation instances.
Store vtkAlgorithm input/output information.
Read molecular data files.
unsigned int MakeBonds(vtkPoints *points, vtkIdTypeArray *atomTypes, vtkCellArray *newBonds)
Creates molecular bonds (VTK cells) given atomic coordinates (VTK points) and atom types.
vtkSmartPointer< vtkStringArray > AtomTypeStrings
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructures
int FillOutputPortInformation(int, vtkInformation *) override
Fill the output port information objects for this algorithm.
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
vtkSmartPointer< vtkIdTypeArray > Residue
vtkSetFilePathMacro(FileName)
int RequestData(vtkInformation *, vtkInformationVector **, vtkInformationVector *) override
This is called by the superclass.
vtkGetFilePathMacro(FileName)
unsigned int MakeAtomType(const char *atomType)
Given a string for the type (name) of an atom, returns a unique number for that atom.
vtkSmartPointer< vtkUnsignedCharArray > RGB
virtual void ReadSpecificMolecule(FILE *fp)=0
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructuresEnd
vtkSmartPointer< vtkPoints > Points
int ReadMolecule(FILE *fp, vtkPolyData *output)
Reads a molecule from the passed file pointer and creates a vtkPolyData.
vtkNew< vtkPeriodicTable > PeriodicTable
vtkSmartPointer< vtkUnsignedCharArray > SecondaryStructuresBegin
vtkSmartPointer< vtkIdTypeArray > AtomType
vtkSmartPointer< vtkUnsignedIntArray > Model
vtkSmartPointer< vtkUnsignedCharArray > IsHetatm
vtkSmartPointer< vtkUnsignedCharArray > Chain
vtkSmartPointer< vtkMolecule > Molecule
~vtkMoleculeReaderBase() override
vtkSmartPointer< vtkFloatArray > Radii
class describing a molecule
Definition: vtkMolecule.h:92
Access to information about the elements.
represent and manipulate 3D points
Definition: vtkPoints.h:34
Superclass for algorithms that produce only polydata as output.
concrete dataset represents vertices, lines, polygons, and triangle strips
Definition: vtkPolyData.h:86
a vtkAbstractArray subclass for strings
dynamic, self-adjusting array of unsigned char
dynamic, self-adjusting array of unsigned int
@ points
Definition: vtkX3D.h:452
int vtkIdType
Definition: vtkType.h:332